/*
 * Copyright (c) 2011 Seoul National University
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met: redistributions of source code must retain the above copyright
 * notice, this list of conditions and the following disclaimer;
 * redistributions in binary form must reproduce the above copyright
 * notice, this list of conditions and the following disclaimer in the
 * documentation and/or other materials provided with the distribution;
 * neither the name of the copyright holders nor the names of its
 * contributors may be used to endorse or promote products derived from
 * this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * Authors: Jung Ho Ahn  ( gajh@snu.ac.kr )
 *
 */

#ifndef __GRAPH_H__
#define __GRAPH_H__

#include "KmerHashTable.h"
#include <unordered_set>
#include <set>

using namespace std;

struct ltstrKmerNode
{
  bool operator()(const KmerNode * k1, const KmerNode * k2)
  {
    return k1->getHitCount() < k2->getHitCount();
  }
};


class Graph
{
  public:
    Graph(KmerCoverageTable * table_);
    ~Graph();

    void findLikelyNeighbors();
    void extractContig();
    void resolveConflicts();
    void displayNodes();

  private:
    KmerCoverageTable * table;
    multiset<KmerNode *, ltstrKmerNode> sortedConflicts;
    unordered_set<KmerNode *> conflicts;

    inline double maxDouble(double a, double b) { return (a > b) ? a : b; }
    inline void updateContigHistogram(uint32_t length);

};

#endif  // __GRAPH_H__
